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nc4_data_output.cpp @ 1046

Last change on this file since 1046 was 1046, checked in by ymipsl, 7 years ago

Add 2 new file attributes to parameter timestamp : time_stamp_name and time_stamp_format.

Default value :
time_stamp_name="timestamp"
time_stamp_format="%Y-%b-%d %H:%M:%S %Z"

timestamp is now given in UTC time

Property copyright set to
Software name : XIOS (Xml I/O Server)
http://forge.ipsl.jussieu.fr/ioserver
Creation date : January 2009
Licence : CeCCIL version2
see license file in root directory : Licence_CeCILL_V2-en.txt
or http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
Holder : CEA/LSCE (Laboratoire des Sciences du CLimat et de l'Environnement)
CNRS/IPSL (Institut Pierre Simon Laplace)
Project Manager : Yann Meurdesoif
yann.meurdesoif@cea.fr
Property svn:executable set to *

File size: 116.8 KB

Line
1	#include "nc4_data_output.hpp"
2
3	#include <boost/lexical_cast.hpp>
4	#include "attribute_template.hpp"
5	#include "group_template.hpp"
6
7	#include "file.hpp"
8	#include "calendar.hpp"
9	#include "context.hpp"
10	#include "context_server.hpp"
11	#include "netCdfException.hpp"
12	#include "exception.hpp"
13
14	namespace xios
15	{
16	/// ////////////////////// Dfinitions ////////////////////// ///
17	CNc4DataOutput::CNc4DataOutput
18	(CFile* file, const StdString & filename, bool exist)
19	: SuperClass()
20	, SuperClassWriter(filename, exist)
21	, filename(filename)
22	, file(file)
23	{
24	SuperClass::type = MULTI_FILE;
25	}
26
27	CNc4DataOutput::CNc4DataOutput
28	(CFile* file, const StdString & filename, bool exist, bool useClassicFormat, bool useCFConvention,
29	MPI_Comm comm_file, bool multifile, bool isCollective, const StdString& timeCounterName)
30	: SuperClass()
31	, SuperClassWriter(filename, exist, useClassicFormat, useCFConvention, &comm_file, multifile, timeCounterName)
32	, comm_file(comm_file)
33	, filename(filename)
34	, isCollective(isCollective)
35	, file(file)
36	{
37	SuperClass::type = (multifile) ? MULTI_FILE : ONE_FILE;
38	}
39
40	CNc4DataOutput::~CNc4DataOutput(void)
41	{ /* Ne rien faire de plus */ }
42
43	///--------------------------------------------------------------
44
45	const StdString & CNc4DataOutput::getFileName(void) const
46	{
47	return (this->filename);
48	}
49
50	//---------------------------------------------------------------
51
52	void CNc4DataOutput::writeDomain_(CDomain* domain)
53	{
54	if (domain->type == CDomain::type_attr::unstructured)
55	{
56	if (SuperClassWriter::useCFConvention)
57	writeUnstructuredDomain(domain) ;
58	else
59	writeUnstructuredDomainUgrid(domain) ;
60	return ;
61	}
62
63	CContext* context = CContext::getCurrent() ;
64	CContextServer* server=context->server ;
65
66	if (domain->IsWritten(this->filename)) return;
67	domain->checkAttributes();
68
69	if (domain->isEmpty())
70	if (SuperClass::type==MULTI_FILE) return;
71
72	std::vector<StdString> dim0, dim1;
73	StdString domid = domain->getDomainOutputName();
74	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
75	if (isWrittenDomain(domid)) return ;
76	else setWrittenDomain(domid);
77
78
79	StdString dimXid, dimYid ;
80
81	nc_type typePrec ;
82	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
83	else if (domain->prec==4) typePrec = NC_FLOAT ;
84	else if (domain->prec==8) typePrec = NC_DOUBLE ;
85
86	bool isRegularDomain = (domain->type == CDomain::type_attr::rectilinear);
87	switch (domain->type)
88	{
89	case CDomain::type_attr::curvilinear :
90	dimXid = StdString("x").append(appendDomid);
91	dimYid = StdString("y").append(appendDomid);
92	break ;
93	case CDomain::type_attr::rectilinear :
94	dimXid = StdString("lon").append(appendDomid);
95	dimYid = StdString("lat").append(appendDomid);
96	break;
97	}
98
99	StdString dimVertId = StdString("nvertex").append(appendDomid);
100
101	string lonid,latid,bounds_lonid,bounds_latid ;
102	string areaId = "area" + appendDomid;
103	/*
104	StdString lonid_loc = (server->intraCommSize > 1)
105	? StdString("lon").append(appendDomid).append("_local")
106	: lonid;
107	StdString latid_loc = (server->intraCommSize > 1)
108	? StdString("lat").append(appendDomid).append("_local")
109	: latid;
110	*/
111
112	try
113	{
114	switch (SuperClass::type)
115	{
116	case (MULTI_FILE) :
117	{
118	// if (domain->isEmpty()) return;
119
120	if (server->intraCommSize > 1)
121	{
122	// SuperClassWriter::addDimension(lonid, domain->zoom_ni.getValue());
123	// SuperClassWriter::addDimension(latid, domain->zoom_nj.getValue());
124	}
125
126	switch (domain->type)
127	{
128	case CDomain::type_attr::curvilinear :
129	dim0.push_back(dimYid); dim0.push_back(dimXid);
130	lonid = StdString("nav_lon").append(appendDomid);
131	latid = StdString("nav_lat").append(appendDomid);
132	break ;
133	case CDomain::type_attr::rectilinear :
134	lonid = StdString("lon").append(appendDomid);
135	latid = StdString("lat").append(appendDomid);
136	dim0.push_back(dimYid);
137	dim1.push_back(dimXid);
138	break;
139	}
140
141	bounds_lonid = StdString("bounds_lon").append(appendDomid);
142	bounds_latid = StdString("bounds_lat").append(appendDomid);
143
144	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
145	SuperClassWriter::addDimension(dimYid, domain->zoom_nj_srv);
146
147	if (domain->hasBounds)
148	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
149
150	if (server->intraCommSize > 1)
151	{
152	this->writeLocalAttributes(domain->zoom_ibegin_srv,
153	domain->zoom_ni_srv,
154	domain->zoom_jbegin_srv,
155	domain->zoom_nj_srv,
156	appendDomid);
157
158	if (singleDomain)
159	this->writeLocalAttributes_IOIPSL(dimXid, dimYid,
160	domain->zoom_ibegin_srv,
161	domain->zoom_ni_srv,
162	domain->zoom_jbegin_srv,
163	domain->zoom_nj_srv,
164	domain->ni_glo,domain->nj_glo,
165	server->intraCommRank,server->intraCommSize);
166	}
167
168	if (domain->hasLonLat)
169	{
170	switch (domain->type)
171	{
172	case CDomain::type_attr::curvilinear :
173	SuperClassWriter::addVariable(latid, typePrec, dim0);
174	SuperClassWriter::addVariable(lonid, typePrec, dim0);
175	break ;
176	case CDomain::type_attr::rectilinear :
177	SuperClassWriter::addVariable(latid, typePrec, dim0);
178	SuperClassWriter::addVariable(lonid, typePrec, dim1);
179	break ;
180	}
181
182	this->writeAxisAttributes(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
183	this->writeAxisAttributes(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
184
185	if (domain->hasBounds)
186	{
187	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
188	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
189
190	dim0.clear();
191	dim0.push_back(dimYid);
192	dim0.push_back(dimXid);
193	dim0.push_back(dimVertId);
194	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
195	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
196	}
197	}
198
199	dim0.clear();
200	dim0.push_back(dimYid);
201	dim0.push_back(dimXid);
202
203
204	// supress mask if (server->intraCommSize > 1)
205	// supress mask {
206	// supress mask SuperClassWriter::addVariable(maskid, NC_INT, dim0);
207	// supress mask
208	// supress mask this->writeMaskAttributes(maskid,
209	// supress mask domain->data_dim.getValue()/*,
210	// supress mask domain->data_ni.getValue(),
211	// supress mask domain->data_nj.getValue(),
212	// supress mask domain->data_ibegin.getValue(),
213	// supress mask domain->data_jbegin.getValue()*/);
214	// supress mask }
215
216	//SuperClassWriter::setDefaultValue(maskid, &dvm);
217
218	if (domain->hasArea)
219	{
220	SuperClassWriter::addVariable(areaId, typePrec, dim0);
221	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
222	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
223	}
224
225	SuperClassWriter::definition_end();
226
227	if (domain->hasLonLat)
228	{
229	switch (domain->type)
230	{
231	case CDomain::type_attr::curvilinear :
232	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
233	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
234	break;
235	case CDomain::type_attr::rectilinear :
236	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
237	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0);
238	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
239	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0);
240	break;
241	}
242
243	if (domain->hasBounds)
244	{
245	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
246	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
247	}
248	}
249
250	if (domain->hasArea)
251	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
252
253	SuperClassWriter::definition_start();
254
255	break;
256	}
257	case (ONE_FILE) :
258	{
259	SuperClassWriter::addDimension(dimXid, domain->global_zoom_ni);
260	SuperClassWriter::addDimension(dimYid, domain->global_zoom_nj);
261
262	if (domain->hasBounds)
263	SuperClassWriter::addDimension(dimVertId, domain->nvertex);
264
265	if (domain->hasLonLat)
266	{
267	switch (domain->type)
268	{
269	case CDomain::type_attr::curvilinear :
270	dim0.push_back(dimYid); dim0.push_back(dimXid);
271	lonid = StdString("nav_lon").append(appendDomid);
272	latid = StdString("nav_lat").append(appendDomid);
273	SuperClassWriter::addVariable(latid, typePrec, dim0);
274	SuperClassWriter::addVariable(lonid, typePrec, dim0);
275	break;
276
277	case CDomain::type_attr::rectilinear :
278	dim0.push_back(dimYid);
279	dim1.push_back(dimXid);
280	lonid = StdString("lon").append(appendDomid);
281	latid = StdString("lat").append(appendDomid);
282	SuperClassWriter::addVariable(latid, typePrec, dim0);
283	SuperClassWriter::addVariable(lonid, typePrec, dim1);
284	break;
285	}
286
287	bounds_lonid = StdString("bounds_lon").append(appendDomid);
288	bounds_latid = StdString("bounds_lat").append(appendDomid);
289
290	this->writeAxisAttributes
291	(lonid, isRegularDomain ? "X" : "", "longitude", "Longitude", "degrees_east", domid);
292	this->writeAxisAttributes
293	(latid, isRegularDomain ? "Y" : "", "latitude", "Latitude", "degrees_north", domid);
294
295	if (domain->hasBounds)
296	{
297	SuperClassWriter::addAttribute("bounds", bounds_lonid, &lonid);
298	SuperClassWriter::addAttribute("bounds", bounds_latid, &latid);
299
300	dim0.clear();
301	dim0.push_back(dimYid);
302	dim0.push_back(dimXid);
303	dim0.push_back(dimVertId);
304	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
305	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
306	}
307	}
308
309	if (domain->hasArea)
310	{
311	dim0.clear();
312	dim0.push_back(dimYid); dim0.push_back(dimXid);
313	SuperClassWriter::addVariable(areaId, typePrec, dim0);
314	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
315	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
316	dim0.clear();
317	}
318
319	SuperClassWriter::definition_end();
320
321	switch (domain->type)
322	{
323	case CDomain::type_attr::curvilinear :
324	{
325	std::vector<StdSize> start(2) ;
326	std::vector<StdSize> count(2) ;
327	if (domain->isEmpty())
328	{
329	start[0]=0 ; start[1]=0 ;
330	count[0]=0 ; count[1]=0 ;
331	}
332	else
333	{
334	start[1]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
335	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
336	count[1]=domain->zoom_ni_srv ; count[0]=domain->zoom_nj_srv ;
337	}
338
339	if (domain->hasLonLat)
340	{
341	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
342	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
343	}
344	break;
345	}
346	case CDomain::type_attr::rectilinear :
347	{
348	if (domain->hasLonLat)
349	{
350	std::vector<StdSize> start(1) ;
351	std::vector<StdSize> count(1) ;
352	if (domain->isEmpty())
353	{
354	start[0]=0 ;
355	count[0]=0 ;
356	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
357	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
358
359	}
360	else
361	{
362	start[0]=domain->zoom_jbegin_srv-domain->global_zoom_jbegin;
363	count[0]=domain->zoom_nj_srv ;
364	CArray<double,1> lat = domain->latvalue_srv(Range(fromStart,toEnd,domain->zoom_ni_srv)) ;
365	SuperClassWriter::writeData(CArray<double,1>(lat.copy()), latid, isCollective, 0,&start,&count);
366
367	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
368	count[0]=domain->zoom_ni_srv ;
369	CArray<double,1> lon=domain->lonvalue_srv(Range(0,domain->zoom_ni_srv-1)) ;
370	SuperClassWriter::writeData(CArray<double,1>(lon.copy()), lonid, isCollective, 0,&start,&count);
371	}
372	}
373	break;
374	}
375	}
376
377	if (domain->hasBounds)
378	{
379	std::vector<StdSize> start(3);
380	std::vector<StdSize> count(3);
381	if (domain->isEmpty())
382	{
383	start[2] = start[1] = start[0] = 0;
384	count[2] = count[1] = count[0] = 0;
385	}
386	else
387	{
388	start[2] = 0;
389	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
390	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
391	count[2] = domain->nvertex;
392	count[1] = domain->zoom_ni_srv;
393	count[0] = domain->zoom_nj_srv;
394	}
395
396	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0, &start, &count);
397	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0, &start, &count);
398	}
399
400	if (domain->hasArea)
401	{
402	std::vector<StdSize> start(2);
403	std::vector<StdSize> count(2);
404
405	if (domain->isEmpty())
406	{
407	start[0] = 0; start[1] = 0;
408	count[0] = 0; count[1] = 0;
409	}
410	else
411	{
412	start[1] = domain->zoom_ibegin_srv - domain->global_zoom_ibegin;
413	start[0] = domain->zoom_jbegin_srv - domain->global_zoom_jbegin;
414	count[1] = domain->zoom_ni_srv;
415	count[0] = domain->zoom_nj_srv;
416	}
417
418	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
419	}
420
421	SuperClassWriter::definition_start();
422	break;
423	}
424	default :
425	ERROR("CNc4DataOutput::writeDomain(domain)",
426	<< "[ type = " << SuperClass::type << "]"
427	<< " not implemented yet !");
428	}
429	}
430	catch (CNetCdfException& e)
431	{
432	StdString msg("On writing the domain : ");
433	msg.append(domid); msg.append("\n");
434	msg.append("In the context : ");
435	msg.append(context->getId()); msg.append("\n");
436	msg.append(e.what());
437	ERROR("CNc4DataOutput::writeDomain_(CDomain* domain)", << msg);
438	}
439
440	domain->addRelFile(this->filename);
441	}
442
443	//--------------------------------------------------------------
444
445	void CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)
446	{
447	CContext* context = CContext::getCurrent() ;
448	CContextServer* server=context->server ;
449
450	if (domain->IsWritten(this->filename)) return;
451	domain->checkAttributes();
452	if (domain->isEmpty())
453	if (SuperClass::type==MULTI_FILE) return ;
454
455	nc_type typePrec ;
456	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
457	else if (domain->prec==4) typePrec = NC_FLOAT ;
458	else if (domain->prec==8) typePrec = NC_DOUBLE ;
459
460	std::vector<StdString> dim0;
461	StdString domid = domain->getDomainOutputName();
462	StdString domainName = domain->name;
463	domain->assignMesh(domainName, domain->nvertex);
464	domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
465
466	StdString node_x = domainName + "_node_x";
467	StdString node_y = domainName + "_node_y";
468
469	StdString edge_x = domainName + "_edge_x";
470	StdString edge_y = domainName + "_edge_y";
471	StdString edge_nodes = domainName + "_edge_nodes";
472
473	StdString face_x = domainName + "_face_x";
474	StdString face_y = domainName + "_face_y";
475	StdString face_nodes = domainName + "_face_nodes";
476	StdString face_edges = domainName + "_face_edges";
477	StdString edge_faces = domainName + "_edge_face_links";
478	StdString face_faces = domainName + "_face_links";
479
480	StdString dimNode = "n" + domainName + "_node";
481	StdString dimEdge = "n" + domainName + "_edge";
482	StdString dimFace = "n" + domainName + "_face";
483	StdString dimVertex = "n" + domainName + "_vertex";
484	StdString dimTwo = "Two";
485
486	if (!SuperClassWriter::dimExist(dimTwo)) SuperClassWriter::addDimension(dimTwo, 2);
487	if (!isWrittenDomain(domid))
488	{
489	dim0.clear();
490	SuperClassWriter::addVariable(domainName, NC_INT, dim0);
491	SuperClassWriter::addAttribute("cf_role", StdString("mesh_topology"), &domainName);
492	SuperClassWriter::addAttribute("long_name", StdString("Topology data of 2D unstructured mesh"), &domainName);
493	SuperClassWriter::addAttribute("topology_dimension", 2, &domainName);
494	SuperClassWriter::addAttribute("node_coordinates", node_x + " " + node_y, &domainName);
495	}
496
497	try
498	{
499	switch (SuperClass::type)
500	{
501	case (ONE_FILE) :
502	{
503	// Adding nodes
504	if (domain->nvertex == 1)
505	{
506	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
507	{
508	SuperClassWriter::addDimension(dimNode, domain->ni_glo);
509	dim0.clear();
510	dim0.push_back(dimNode);
511	SuperClassWriter::addVariable(node_x, typePrec, dim0);
512	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
513	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
514	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
515	SuperClassWriter::addVariable(node_y, typePrec, dim0);
516	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
517	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
518	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
519	}
520	} // domain->nvertex == 1
521
522	// Adding edges and nodes, if nodes have not been defined previously
523	if (domain->nvertex == 2)
524	{
525	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
526	{
527	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
528	dim0.clear();
529	dim0.push_back(dimNode);
530	SuperClassWriter::addVariable(node_x, typePrec, dim0);
531	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
532	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
533	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
534	SuperClassWriter::addVariable(node_y, typePrec, dim0);
535	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
536	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
537	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
538	}
539	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
540	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
541	SuperClassWriter::addDimension(dimEdge, domain->ni_glo);
542	dim0.clear();
543	dim0.push_back(dimEdge);
544	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
545	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
546	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
547	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
548	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
549	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
550	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
551	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
552	dim0.clear();
553	dim0.push_back(dimEdge);
554	dim0.push_back(dimTwo);
555	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
556	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
557	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
558	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
559	} // domain->nvertex == 2
560
561	// Adding faces, edges, and nodes, if edges and nodes have not been defined previously
562	if (domain->nvertex > 2)
563	{
564	// Nodes
565	if (!SuperClassWriter::varExist(node_x) \|\| !SuperClassWriter::varExist(node_y))
566	{
567	SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodesGlo);
568	dim0.clear();
569	dim0.push_back(dimNode);
570	SuperClassWriter::addVariable(node_x, typePrec, dim0);
571	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
572	SuperClassWriter::addAttribute("long_name", StdString("Longitude of mesh nodes."), &node_x);
573	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
574	SuperClassWriter::addVariable(node_y, typePrec, dim0);
575	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
576	SuperClassWriter::addAttribute("long_name", StdString("Latitude of mesh nodes."), &node_y);
577	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
578	}
579	if (!SuperClassWriter::varExist(edge_x) \|\| !SuperClassWriter::varExist(edge_y))
580	{
581	SuperClassWriter::addAttribute("edge_coordinates", edge_x + " " + edge_y, &domainName);
582	SuperClassWriter::addAttribute("edge_node_connectivity", edge_nodes, &domainName);
583	SuperClassWriter::addDimension(dimEdge, domain->mesh->nbEdgesGlo);
584	dim0.clear();
585	dim0.push_back(dimEdge);
586	SuperClassWriter::addVariable(edge_x, typePrec, dim0);
587	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &edge_x);
588	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh edges."), &edge_x);
589	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &edge_x);
590	SuperClassWriter::addVariable(edge_y, typePrec, dim0);
591	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &edge_y);
592	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh edges."), &edge_y);
593	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &edge_y);
594	dim0.clear();
595	dim0.push_back(dimEdge);
596	dim0.push_back(dimTwo);
597	SuperClassWriter::addVariable(edge_nodes, NC_INT, dim0);
598	SuperClassWriter::addAttribute("cf_role", StdString("edge_node_connectivity"), &edge_nodes);
599	SuperClassWriter::addAttribute("long_name", StdString("Maps every edge/link to two nodes that it connects."), &edge_nodes);
600	SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
601	}
602	SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
603	SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
604	SuperClassWriter::addDimension(dimFace, domain->ni_glo);
605	SuperClassWriter::addDimension(dimVertex, domain->nvertex);
606	dim0.clear();
607	dim0.push_back(dimFace);
608	SuperClassWriter::addVariable(face_x, typePrec, dim0);
609	SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &face_x);
610	SuperClassWriter::addAttribute("long_name", StdString("Characteristic longitude of mesh faces."), &face_x);
611	SuperClassWriter::addAttribute("units", StdString("degrees_east"), &face_x);
612	SuperClassWriter::addVariable(face_y, typePrec, dim0);
613	SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &face_y);
614	SuperClassWriter::addAttribute("long_name", StdString("Characteristic latitude of mesh faces."), &face_y);
615	SuperClassWriter::addAttribute("units", StdString("degrees_north"), &face_y);
616	dim0.clear();
617	dim0.push_back(dimFace);
618	dim0.push_back(dimVertex);
619	SuperClassWriter::addVariable(face_nodes, NC_INT, dim0);
620	SuperClassWriter::addAttribute("cf_role", StdString("face_node_connectivity"), &face_nodes);
621	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
622	SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
623	dim0.clear();
624	dim0.push_back(dimFace);
625	dim0.push_back(dimVertex);
626	SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
627	SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
628	SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
629	SuperClassWriter::addAttribute("start_index", 0, &face_edges);
630	SuperClassWriter::addAttribute("_FillValue", 999999, &face_edges);
631	dim0.clear();
632	dim0.push_back(dimEdge);
633	dim0.push_back(dimTwo);
634	SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
635	SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
636	SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
637	SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
638	SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
639	SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
640	dim0.clear();
641	dim0.push_back(dimFace);
642	dim0.push_back(dimVertex);
643	SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
644	SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
645	SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
646	SuperClassWriter::addAttribute("start_index", 0, &face_faces);
647	SuperClassWriter::addAttribute("_FillValue", 999999, &face_faces);
648	SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
649	SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
650	} // domain->nvertex > 2
651
652	SuperClassWriter::definition_end();
653
654	std::vector<StdSize> startEdges(1) ;
655	std::vector<StdSize> countEdges(1) ;
656	std::vector<StdSize> startNodes(1) ;
657	std::vector<StdSize> countNodes(1) ;
658	std::vector<StdSize> startFaces(1) ;
659	std::vector<StdSize> countFaces(1) ;
660	std::vector<StdSize> startEdgeNodes(2) ;
661	std::vector<StdSize> countEdgeNodes(2) ;
662	std::vector<StdSize> startEdgeFaces(2) ;
663	std::vector<StdSize> countEdgeFaces(2) ;
664	std::vector<StdSize> startFaceConctv(2) ;
665	std::vector<StdSize> countFaceConctv(2) ;
666
667	if (!isWrittenDomain(domid))
668	{
669	if (domain->nvertex == 1)
670	{
671	if (domain->isEmpty())
672	{
673	startNodes[0]=0 ;
674	countNodes[0]=0 ;
675	}
676	else
677	{
678	startNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
679	countNodes[0] = domain->zoom_ni_srv ;
680	}
681
682	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
683	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
684	}
685	else if (domain->nvertex == 2)
686	{
687	if (domain->isEmpty())
688	{
689	startEdges[0]=0 ;
690	countEdges[0]=0 ;
691	startNodes[0]=0 ;
692	countNodes[0]=0 ;
693	startEdgeNodes[0]=0;
694	startEdgeNodes[1]=0;
695	countEdgeNodes[0]=0;
696	countEdgeNodes[1]=0;
697
698	}
699	else
700	{
701	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
702	countEdges[0] = domain->zoom_ni_srv ;
703	startNodes[0] = domain->mesh->node_start;
704	countNodes[0] = domain->mesh->node_count;
705	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
706	startEdgeNodes[1] = 0;
707	countEdgeNodes[0] = domain->zoom_ni_srv;
708	countEdgeNodes[1]= 2;
709	}
710	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
711	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
712	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
713	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
714	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
715	}
716	else
717	{
718	if (domain->isEmpty())
719	{
720	startFaces[0] = 0 ;
721	countFaces[0] = 0 ;
722	startNodes[0] = 0;
723	countNodes[0] = 0;
724	startEdges[0] = 0;
725	countEdges[0] = 0;
726	startEdgeFaces[0] = 0;
727	startEdgeFaces[1] = 0;
728	countEdgeFaces[0] = 0;
729	countEdgeFaces[1] = 0;
730	startFaceConctv[0] = 0;
731	startFaceConctv[1] = 0;
732	countFaceConctv[0] = 0;
733	countFaceConctv[1] = 0;
734	}
735	else
736	{
737	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
738	countFaces[0] = domain->zoom_ni_srv ;
739	startNodes[0] = domain->mesh->node_start;
740	countNodes[0] = domain->mesh->node_count;
741	startEdges[0] = domain->mesh->edge_start;
742	countEdges[0] = domain->mesh->edge_count;
743	startEdgeNodes[0] = domain->mesh->edge_start;
744	startEdgeNodes[1] = 0;
745	countEdgeNodes[0] = domain->mesh->edge_count;
746	countEdgeNodes[1]= 2;
747	startEdgeFaces[0] = domain->mesh->edge_start;
748	startEdgeFaces[1]= 0;
749	countEdgeFaces[0] = domain->mesh->edge_count;
750	countEdgeFaces[1]= 2;
751	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
752	startFaceConctv[1] = 0;
753	countFaceConctv[0] = domain->zoom_ni_srv;
754	countFaceConctv[1] = domain->nvertex;
755	}
756	SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &startNodes, &countNodes);
757	SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &startNodes, &countNodes);
758	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
759	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
760	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
761	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
762	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
763	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
764	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
765	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
766	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
767	}
768	setWrittenDomain(domid);
769	} // !isWrittenDomain
770	else
771	{
772	if (domain->nvertex == 2)
773	{
774	startEdges[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
775	countEdges[0] = domain->zoom_ni_srv ;
776	startEdgeNodes[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
777	startEdgeNodes[1] = 0;
778	countEdgeNodes[0] = domain->zoom_ni_srv;
779	countEdgeNodes[1]= 2;
780	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
781	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
782	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
783	}
784	if (domain->nvertex > 2)
785	{
786
787	if (!domain->mesh->edgesAreWritten)
788	{
789	startEdges[0] = domain->mesh->edge_start;
790	countEdges[0] = domain->mesh->edge_count;
791	startEdgeNodes[0] = domain->mesh->edge_start;
792	startEdgeNodes[1] = 0;
793	countEdgeNodes[0] = domain->mesh->edge_count;
794	countEdgeNodes[1]= 2;
795	SuperClassWriter::writeData(domain->mesh->edge_lat, edge_y, isCollective, 0, &startEdges, &countEdges);
796	SuperClassWriter::writeData(domain->mesh->edge_lon, edge_x, isCollective, 0, &startEdges, &countEdges);
797	SuperClassWriter::writeData(domain->mesh->edge_nodes, edge_nodes, isCollective, 0, &startEdgeNodes, &countEdgeNodes);
798	}
799	startFaces[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
800	countFaces[0] = domain->zoom_ni_srv;
801	startEdgeFaces[0] = domain->mesh->edge_start;
802	startEdgeFaces[1]= 0;
803	countEdgeFaces[0] = domain->mesh->edge_count;
804	countEdgeFaces[1]= 2;
805	startFaceConctv[0] = domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
806	startFaceConctv[1] = 0;
807	countFaceConctv[0] = domain->zoom_ni_srv;
808	countFaceConctv[1]= domain->nvertex;
809	SuperClassWriter::writeData(domain->mesh->face_lat, face_y, isCollective, 0, &startFaces, &countFaces);
810	SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0, &startFaces, &countFaces);
811	SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes, isCollective, 0, &startFaceConctv, &countFaceConctv);
812	SuperClassWriter::writeData(domain->mesh->face_edges, face_edges, isCollective, 0, &startFaceConctv, &countFaceConctv);
813	SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces, isCollective, 0, &startEdgeFaces, &countEdgeFaces);
814	SuperClassWriter::writeData(domain->mesh->face_faces, face_faces, isCollective, 0, &startFaceConctv, &countFaceConctv);
815	}
816	}// isWrittenDomain
817
818	SuperClassWriter::definition_start();
819
820	break;
821	} // ONE_FILE
822
823	case (MULTI_FILE) :
824	{
825	break;
826	}
827
828	default :
829	ERROR("CNc4DataOutput::writeDomain(domain)",
830	<< "[ type = " << SuperClass::type << "]"
831	<< " not implemented yet !");
832	} // switch
833	} // try
834
835	catch (CNetCdfException& e)
836	{
837	StdString msg("On writing the domain : ");
838	msg.append(domid); msg.append("\n");
839	msg.append("In the context : ");
840	msg.append(context->getId()); msg.append("\n");
841	msg.append(e.what());
842	ERROR("CNc4DataOutput::writeUnstructuredDomainUgrid(CDomain* domain)", << msg);
843	}
844
845	domain->addRelFile(this->filename);
846	}
847
848	//--------------------------------------------------------------
849
850	void CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)
851	{
852	CContext* context = CContext::getCurrent() ;
853	CContextServer* server=context->server ;
854
855	if (domain->IsWritten(this->filename)) return;
856	domain->checkAttributes();
857
858	if (domain->isEmpty())
859	if (SuperClass::type==MULTI_FILE) return ;
860
861	std::vector<StdString> dim0, dim1;
862	StdString domid = domain->getDomainOutputName();
863	if (isWrittenDomain(domid)) return ;
864	else setWrittenDomain(domid);
865
866	StdString appendDomid = (singleDomain) ? "" : "_"+domid ;
867
868	StdString dimXid = StdString("cell").append(appendDomid);
869	StdString dimVertId = StdString("nvertex").append(appendDomid);
870
871	string lonid,latid,bounds_lonid,bounds_latid ;
872	string areaId = "area" + appendDomid;
873
874	nc_type typePrec ;
875	if (domain->prec.isEmpty()) typePrec = NC_FLOAT ;
876	else if (domain->prec==4) typePrec = NC_FLOAT ;
877	else if (domain->prec==8) typePrec = NC_DOUBLE ;
878
879	try
880	{
881	switch (SuperClass::type)
882	{
883	case (MULTI_FILE) :
884	{
885	dim0.push_back(dimXid);
886	SuperClassWriter::addDimension(dimXid, domain->zoom_ni_srv);
887
888	lonid = StdString("lon").append(appendDomid);
889	latid = StdString("lat").append(appendDomid);
890	bounds_lonid = StdString("bounds_lon").append(appendDomid);
891	bounds_latid = StdString("bounds_lat").append(appendDomid);
892	if (domain->hasLonLat)
893	{
894	SuperClassWriter::addVariable(latid, typePrec, dim0);
895	SuperClassWriter::addVariable(lonid, typePrec, dim0);
896	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
897	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
898	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
899	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
900	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
901	}
902	dim0.clear();
903	if (domain->hasBounds)
904	{
905	dim0.push_back(dimXid);
906	dim0.push_back(dimVertId);
907	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
908	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
909	}
910
911	dim0.clear();
912	dim0.push_back(dimXid);
913	if (domain->hasArea)
914	{
915	SuperClassWriter::addVariable(areaId, typePrec, dim0);
916	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
917	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
918	}
919
920	SuperClassWriter::definition_end();
921
922	if (domain->hasLonLat)
923	{
924	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0);
925	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0);
926	if (domain->hasBounds)
927	{
928	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0);
929	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0);
930	}
931	}
932
933	if (domain->hasArea)
934	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0);
935
936	SuperClassWriter::definition_start();
937	break ;
938	}
939
940	case (ONE_FILE) :
941	{
942	lonid = StdString("lon").append(appendDomid);
943	latid = StdString("lat").append(appendDomid);
944	bounds_lonid = StdString("bounds_lon").append(appendDomid);
945	bounds_latid = StdString("bounds_lat").append(appendDomid);
946	dim0.push_back(dimXid);
947	SuperClassWriter::addDimension(dimXid, domain->ni_glo);
948	if (domain->hasLonLat)
949	{
950	SuperClassWriter::addVariable(latid, typePrec, dim0);
951	SuperClassWriter::addVariable(lonid, typePrec, dim0);
952
953	this->writeAxisAttributes(lonid, "", "longitude", "Longitude", "degrees_east", domid);
954	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_lonid, &lonid);
955	this->writeAxisAttributes(latid, "", "latitude", "Latitude", "degrees_north", domid);
956	if (domain->hasBounds) SuperClassWriter::addAttribute("bounds",bounds_latid, &latid);
957	if (domain->hasBounds) SuperClassWriter::addDimension(dimVertId, domain->nvertex);
958	}
959	dim0.clear();
960
961	if (domain->hasBounds)
962	{
963	dim0.push_back(dimXid);
964	dim0.push_back(dimVertId);
965	SuperClassWriter::addVariable(bounds_lonid, typePrec, dim0);
966	SuperClassWriter::addVariable(bounds_latid, typePrec, dim0);
967	}
968
969	if (domain->hasArea)
970	{
971	dim0.clear();
972	dim0.push_back(dimXid);
973	SuperClassWriter::addVariable(areaId, typePrec, dim0);
974	SuperClassWriter::addAttribute("standard_name", StdString("cell_area"), &areaId);
975	SuperClassWriter::addAttribute("units", StdString("m2"), &areaId);
976	}
977
978	SuperClassWriter::definition_end();
979
980	std::vector<StdSize> start(1), startBounds(2) ;
981	std::vector<StdSize> count(1), countBounds(2) ;
982	if (domain->isEmpty())
983	{
984	start[0]=0 ;
985	count[0]=0 ;
986	startBounds[1]=0 ;
987	countBounds[1]=domain->nvertex ;
988	startBounds[0]=0 ;
989	countBounds[0]=0 ;
990	}
991	else
992	{
993	start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
994	count[0]=domain->zoom_ni_srv ;
995	startBounds[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
996	startBounds[1]=0 ;
997	countBounds[0]=domain->zoom_ni_srv ;
998	countBounds[1]=domain->nvertex ;
999	}
1000
1001	if (domain->hasLonLat)
1002	{
1003	SuperClassWriter::writeData(domain->latvalue_srv, latid, isCollective, 0,&start,&count);
1004	SuperClassWriter::writeData(domain->lonvalue_srv, lonid, isCollective, 0,&start,&count);
1005	if (domain->hasBounds)
1006	{
1007	SuperClassWriter::writeData(domain->bounds_lon_srv, bounds_lonid, isCollective, 0,&startBounds,&countBounds);
1008	SuperClassWriter::writeData(domain->bounds_lat_srv, bounds_latid, isCollective, 0,&startBounds,&countBounds);
1009	}
1010	}
1011
1012	if (domain->hasArea)
1013	SuperClassWriter::writeData(domain->area_srv, areaId, isCollective, 0, &start, &count);
1014
1015	SuperClassWriter::definition_start();
1016
1017	break;
1018	}
1019	default :
1020	ERROR("CNc4DataOutput::writeDomain(domain)",
1021	<< "[ type = " << SuperClass::type << "]"
1022	<< " not implemented yet !");
1023	}
1024	}
1025	catch (CNetCdfException& e)
1026	{
1027	StdString msg("On writing the domain : ");
1028	msg.append(domid); msg.append("\n");
1029	msg.append("In the context : ");
1030	msg.append(context->getId()); msg.append("\n");
1031	msg.append(e.what());
1032	ERROR("CNc4DataOutput::writeUnstructuredDomain(CDomain* domain)", << msg);
1033	}
1034	domain->addRelFile(this->filename);
1035	}
1036	//--------------------------------------------------------------
1037
1038	void CNc4DataOutput::writeAxis_(CAxis* axis)
1039	{
1040	if (axis->IsWritten(this->filename)) return;
1041	axis->checkAttributes();
1042	int zoom_size_srv = axis->zoom_size_srv;
1043	int zoom_begin_srv = axis->zoom_begin_srv;
1044	int zoom_size = (MULTI_FILE == SuperClass::type) ? zoom_size_srv
1045	: axis->global_zoom_n;
1046	int zoom_begin = (MULTI_FILE == SuperClass::type) ? zoom_begin_srv
1047	: axis->global_zoom_begin;
1048
1049	if ((0 == zoom_size_srv) && (MULTI_FILE == SuperClass::type)) return;
1050
1051	std::vector<StdString> dims;
1052	StdString axisid = axis->getAxisOutputName();
1053	if (isWrittenAxis(axisid)) return ;
1054	else setWrittenAxis(axisid);
1055
1056	nc_type typePrec ;
1057	if (axis->prec.isEmpty()) typePrec = NC_FLOAT ;
1058	else if (axis->prec==4) typePrec = NC_FLOAT ;
1059	else if (axis->prec==8) typePrec = NC_DOUBLE ;
1060
1061	try
1062	{
1063	SuperClassWriter::addDimension(axisid, zoom_size);
1064	if (axis->hasValue)
1065	{
1066	dims.push_back(axisid);
1067	SuperClassWriter::addVariable(axisid, typePrec, dims);
1068
1069	if (!axis->name.isEmpty())
1070	SuperClassWriter::addAttribute("name", axis->name.getValue(), &axisid);
1071
1072	if (!axis->standard_name.isEmpty())
1073	SuperClassWriter::addAttribute("standard_name", axis->standard_name.getValue(), &axisid);
1074
1075	if (!axis->long_name.isEmpty())
1076	SuperClassWriter::addAttribute("long_name", axis->long_name.getValue(), &axisid);
1077
1078	if (!axis->unit.isEmpty())
1079	SuperClassWriter::addAttribute("units", axis->unit.getValue(), &axisid);
1080
1081	if (!axis->positive.isEmpty())
1082	{
1083	SuperClassWriter::addAttribute("axis", string("Z"), &axisid);
1084	SuperClassWriter::addAttribute("positive",
1085	(axis->positive == CAxis::positive_attr::up) ? string("up") : string("down"),
1086	&axisid);
1087	}
1088
1089	StdString axisBoundsId = axisid + "_bounds";
1090	if (!axis->bounds.isEmpty())
1091	{
1092	dims.push_back("axis_nbounds");
1093	SuperClassWriter::addVariable(axisBoundsId, typePrec, dims);
1094	SuperClassWriter::addAttribute("bounds", axisBoundsId, &axisid);
1095	}
1096
1097	SuperClassWriter::definition_end();
1098
1099	switch (SuperClass::type)
1100	{
1101	case MULTI_FILE:
1102	{
1103	CArray<double,1> axis_value(zoom_size_srv);
1104	for (int i = 0; i < zoom_size_srv; i++) axis_value(i) = axis->value_srv(i);
1105	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0);
1106
1107	if (!axis->bounds.isEmpty())
1108	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0);
1109
1110	SuperClassWriter::definition_start();
1111
1112	break;
1113	}
1114	case ONE_FILE:
1115	{
1116	CArray<double,1> axis_value(zoom_size_srv);
1117	axis_value = axis->value_srv;
1118
1119	std::vector<StdSize> start(1), startBounds(2) ;
1120	std::vector<StdSize> count(1), countBounds(2) ;
1121	start[0] = startBounds[0] = zoom_begin_srv-axis->global_zoom_begin;
1122	count[0] = countBounds[0] = zoom_size_srv;
1123	startBounds[1] = 0;
1124	countBounds[1] = 2;
1125	SuperClassWriter::writeData(axis_value, axisid, isCollective, 0, &start, &count);
1126
1127	if (!axis->bounds.isEmpty())
1128	SuperClassWriter::writeData(axis->bound_srv, axisBoundsId, isCollective, 0, &startBounds, &countBounds);
1129
1130	SuperClassWriter::definition_start();
1131
1132	break;
1133	}
1134	default :
1135	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)",
1136	<< "[ type = " << SuperClass::type << "]"
1137	<< " not implemented yet !");
1138	}
1139	}
1140	}
1141	catch (CNetCdfException& e)
1142	{
1143	StdString msg("On writing the axis : ");
1144	msg.append(axisid); msg.append("\n");
1145	msg.append("In the context : ");
1146	CContext* context = CContext::getCurrent() ;
1147	msg.append(context->getId()); msg.append("\n");
1148	msg.append(e.what());
1149	ERROR("CNc4DataOutput::writeAxis_(CAxis* axis)", << msg);
1150	}
1151	axis->addRelFile(this->filename);
1152	}
1153
1154	void CNc4DataOutput::writeScalar_(CScalar* scalar)
1155	{
1156	if (scalar->IsWritten(this->filename)) return;
1157	scalar->checkAttributes();
1158	int scalarSize = 1;
1159
1160	StdString scalaId = scalar->getScalarOutputName();
1161	if (isWrittenAxis(scalaId)) return ;
1162	else setWrittenAxis(scalaId);
1163
1164	nc_type typePrec ;
1165	if (scalar->prec.isEmpty()) typePrec = NC_FLOAT ;
1166	else if (scalar->prec==4) typePrec = NC_FLOAT ;
1167	else if (scalar->prec==8) typePrec = NC_DOUBLE ;
1168
1169
1170	try
1171	{
1172	if (!scalar->value.isEmpty())
1173	{
1174	// dims.push_back(scalaId);
1175	std::vector<StdString> dims;
1176	SuperClassWriter::addVariable(scalaId, typePrec, dims);
1177
1178	if (!scalar->name.isEmpty())
1179	SuperClassWriter::addAttribute("name", scalar->name.getValue(), &scalaId);
1180
1181	if (!scalar->standard_name.isEmpty())
1182	SuperClassWriter::addAttribute("standard_name", scalar->standard_name.getValue(), &scalaId);
1183
1184	if (!scalar->long_name.isEmpty())
1185	SuperClassWriter::addAttribute("long_name", scalar->long_name.getValue(), &scalaId);
1186
1187	if (!scalar->unit.isEmpty())
1188	SuperClassWriter::addAttribute("units", scalar->unit.getValue(), &scalaId);
1189
1190	SuperClassWriter::definition_end();
1191
1192	switch (SuperClass::type)
1193	{
1194	case MULTI_FILE:
1195	{
1196	CArray<double,1> scalarValue(scalarSize);
1197	scalarValue(0) = scalar->value;
1198	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0);
1199	SuperClassWriter::definition_start();
1200
1201	break;
1202	}
1203	case ONE_FILE:
1204	{
1205	CArray<double,1> scalarValue(scalarSize);
1206	scalarValue(0) = scalar->value;
1207
1208	std::vector<StdSize> start(1);
1209	std::vector<StdSize> count(1);
1210	start[0] = 0;
1211	count[0] = 1;
1212	SuperClassWriter::writeData(scalarValue, scalaId, isCollective, 0, &start, &count);
1213	SuperClassWriter::definition_start();
1214
1215	break;
1216	}
1217	default :
1218	ERROR("CNc4DataOutput::writeAxis_(CAxis* scalar)",
1219	<< "[ type = " << SuperClass::type << "]"
1220	<< " not implemented yet !");
1221	}
1222	}
1223	}
1224	catch (CNetCdfException& e)
1225	{
1226	StdString msg("On writing the scalar : ");
1227	msg.append(scalaId); msg.append("\n");
1228	msg.append("In the context : ");
1229	CContext* context = CContext::getCurrent() ;
1230	msg.append(context->getId()); msg.append("\n");
1231	msg.append(e.what());
1232	ERROR("CNc4DataOutput::writeScalar_(CScalar* scalar)", << msg);
1233	}
1234	scalar->addRelFile(this->filename);
1235	}
1236
1237	//--------------------------------------------------------------
1238
1239	void CNc4DataOutput::writeGridCompressed_(CGrid* grid)
1240	{
1241	if (grid->isScalarGrid() \|\| grid->isWrittenCompressed(this->filename)) return;
1242
1243	try
1244	{
1245	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1246	std::vector<StdString> domainList = grid->getDomainList();
1247	std::vector<StdString> axisList = grid->getAxisList();
1248	std::vector<StdString> scalarList = grid->getScalarList();
1249	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1250
1251	std::vector<StdString> dims;
1252
1253	if (grid->isCompressible())
1254	{
1255	StdString varId = grid->getId() + "_points";
1256
1257	int nbIndexes = (SuperClass::type == MULTI_FILE) ? grid->getNumberWrittenIndexes() : grid->getTotalNumberWrittenIndexes();
1258	SuperClassWriter::addDimension(varId, nbIndexes);
1259
1260	dims.push_back(varId);
1261	SuperClassWriter::addVariable(varId, NC_INT, dims);
1262
1263	StdOStringStream compress;
1264	for (int i = numElement - 1; i >= 0; --i)
1265	{
1266	if (2 == axisDomainOrder(i))
1267	{
1268	CDomain* domain = CDomain::get(domainList[domainList.size() - idxDomain - 1]);
1269	StdString domId = domain->getDomainOutputName();
1270	StdString appendDomId = singleDomain ? "" : "_" + domId;
1271
1272	switch (domain->type)
1273	{
1274	case CDomain::type_attr::curvilinear:
1275	compress << "y" << appendDomId << " x" << appendDomId;
1276	break;
1277	case CDomain::type_attr::rectilinear:
1278	compress << "lat" << appendDomId << " lon" << appendDomId;
1279	break;
1280	case CDomain::type_attr::unstructured:
1281	compress << "cell" << appendDomId;
1282	break;
1283	}
1284	++idxDomain;
1285	}
1286	else if (1 == axisDomainOrder(i))
1287	{
1288	CAxis* axis = CAxis::get(axisList[axisList.size() - idxAxis - 1]);
1289	compress << axis->getAxisOutputName();
1290	++idxAxis;
1291	}
1292	else
1293	{
1294	CScalar* scalar = CScalar::get(scalarList[scalarList.size() - idxScalar - 1]);
1295	compress << scalar->getScalarOutputName();
1296	++idxScalar;
1297	}
1298
1299	if (i != 0) compress << ' ';
1300	}
1301	SuperClassWriter::addAttribute("compress", compress.str(), &varId);
1302
1303	grid->computeCompressedIndex();
1304
1305	CArray<int, 1> indexes(grid->getNumberWrittenIndexes());
1306	std::map<int, CArray<size_t, 1> >::const_iterator it;
1307	for (it = grid->outIndexFromClient.begin(); it != grid->outIndexFromClient.end(); ++it)
1308	{
1309	const CArray<size_t, 1> compressedIndexes = grid->compressedOutIndexFromClient[it->first];
1310	for (int i = 0; i < it->second.numElements(); i++)
1311	indexes(compressedIndexes(i)) = it->second(i);
1312	}
1313
1314	switch (SuperClass::type)
1315	{
1316	case (MULTI_FILE):
1317	{
1318	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1319	break;
1320	}
1321	case (ONE_FILE):
1322	{
1323	if (grid->doGridHaveDataDistributed())
1324	grid->getDistributionServer()->computeGlobalIndex(indexes);
1325
1326	std::vector<StdSize> start, count;
1327	start.push_back(grid->getOffsetWrittenIndexes());
1328	count.push_back(grid->getNumberWrittenIndexes());
1329
1330	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1331	break;
1332	}
1333	}
1334	}
1335	else
1336	{
1337	for (int i = 0; i < numElement; ++i)
1338	{
1339	StdString varId, compress;
1340	CArray<int, 1> indexes;
1341	bool isDistributed;
1342	StdSize nbIndexes, totalNbIndexes, offset;
1343	int firstGlobalIndex;
1344
1345	if (2 == axisDomainOrder(i))
1346	{
1347	CDomain* domain = CDomain::get(domainList[idxDomain]);
1348	StdString domId = domain->getDomainOutputName();
1349
1350	if (!domain->isCompressible()
1351	\|\| domain->type == CDomain::type_attr::unstructured
1352	\|\| domain->isWrittenCompressed(this->filename)
1353	\|\| isWrittenCompressedDomain(domId))
1354	continue;
1355
1356	StdString appendDomId = singleDomain ? "" : "_" + domId;
1357
1358	varId = domId + "_points";
1359	switch (domain->type)
1360	{
1361	case CDomain::type_attr::curvilinear:
1362	compress = "y" + appendDomId + " x" + appendDomId;
1363	break;
1364	case CDomain::type_attr::rectilinear:
1365	compress = "lat" + appendDomId + " lon" + appendDomId;
1366	break;
1367	}
1368
1369	const std::vector<int>& indexesToWrite = domain->getIndexesToWrite();
1370	indexes.resize(indexesToWrite.size());
1371	for (int n = 0; n < indexes.numElements(); ++n)
1372	indexes(n) = indexesToWrite[n];
1373
1374	isDistributed = domain->isDistributed();
1375	nbIndexes = domain->getNumberWrittenIndexes();
1376	totalNbIndexes = domain->getTotalNumberWrittenIndexes();
1377	offset = domain->getOffsetWrittenIndexes();
1378	firstGlobalIndex = domain->ibegin + domain->jbegin * domain->ni_glo;
1379
1380	domain->addRelFileCompressed(this->filename);
1381	setWrittenCompressedDomain(domId);
1382	++idxDomain;
1383	}
1384	else if (1 == axisDomainOrder(i))
1385	{
1386	CAxis* axis = CAxis::get(axisList[idxAxis]);
1387	StdString axisId = axis->getAxisOutputName();
1388
1389	if (!axis->isCompressible()
1390	\|\| axis->isWrittenCompressed(this->filename)
1391	\|\| isWrittenCompressedAxis(axisId))
1392	continue;
1393
1394	varId = axisId + "_points";
1395	compress = axisId;
1396
1397	const std::vector<int>& indexesToWrite = axis->getIndexesToWrite();
1398	indexes.resize(indexesToWrite.size());
1399	for (int n = 0; n < indexes.numElements(); ++n)
1400	indexes(n) = indexesToWrite[n];
1401
1402	isDistributed = axis->isDistributed();
1403	nbIndexes = axis->getNumberWrittenIndexes();
1404	totalNbIndexes = axis->getTotalNumberWrittenIndexes();
1405	offset = axis->getOffsetWrittenIndexes();
1406	firstGlobalIndex = axis->begin;
1407
1408	axis->addRelFileCompressed(this->filename);
1409	setWrittenCompressedAxis(axisId);
1410	++idxAxis;
1411	}
1412	else
1413	{
1414	}
1415
1416	if (!varId.empty())
1417	{
1418	SuperClassWriter::addDimension(varId, (SuperClass::type == MULTI_FILE) ? nbIndexes : totalNbIndexes);
1419
1420	dims.clear();
1421	dims.push_back(varId);
1422	SuperClassWriter::addVariable(varId, NC_INT, dims);
1423
1424	SuperClassWriter::addAttribute("compress", compress, &varId);
1425
1426	switch (SuperClass::type)
1427	{
1428	case (MULTI_FILE):
1429	{
1430	indexes -= firstGlobalIndex;
1431	SuperClassWriter::writeData(indexes, varId, isCollective, 0);
1432	break;
1433	}
1434	case (ONE_FILE):
1435	{
1436	std::vector<StdSize> start, count;
1437	start.push_back(offset);
1438	count.push_back(nbIndexes);
1439
1440	SuperClassWriter::writeData(indexes, varId, isCollective, 0, &start, &count);
1441	break;
1442	}
1443	}
1444	}
1445	}
1446
1447	if (!dims.empty())
1448	grid->computeCompressedIndex();
1449	}
1450
1451	grid->addRelFileCompressed(this->filename);
1452	}
1453	catch (CNetCdfException& e)
1454	{
1455	StdString msg("On writing compressed grid : ");
1456	msg.append(grid->getId()); msg.append("\n");
1457	msg.append("In the context : ");
1458	CContext* context = CContext::getCurrent();
1459	msg.append(context->getId()); msg.append("\n");
1460	msg.append(e.what());
1461	ERROR("CNc4DataOutput::writeGridCompressed_(CGrid* grid)", << msg);
1462	}
1463	}
1464
1465	//--------------------------------------------------------------
1466
1467	void CNc4DataOutput::writeTimeDimension_(void)
1468	{
1469	try
1470	{
1471	SuperClassWriter::addDimension(getTimeCounterName());
1472	}
1473	catch (CNetCdfException& e)
1474	{
1475	StdString msg("On writing time dimension : time_couter\n");
1476	msg.append("In the context : ");
1477	CContext* context = CContext::getCurrent() ;
1478	msg.append(context->getId()); msg.append("\n");
1479	msg.append(e.what());
1480	ERROR("CNc4DataOutput::writeTimeDimension_(void)", << msg);
1481	}
1482	}
1483
1484	//--------------------------------------------------------------
1485
1486	void CNc4DataOutput::writeField_(CField* field)
1487	{
1488	CContext* context = CContext::getCurrent() ;
1489	CContextServer* server=context->server ;
1490
1491	std::vector<StdString> dims, coodinates;
1492	CGrid* grid = field->grid;
1493	if (!grid->doGridHaveDataToWrite())
1494	if (SuperClass::type==MULTI_FILE) return ;
1495
1496	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
1497	int numElement = axisDomainOrder.numElements(), idxDomain = 0, idxAxis = 0, idxScalar = 0;
1498	std::vector<StdString> domainList = grid->getDomainList();
1499	std::vector<StdString> axisList = grid->getAxisList();
1500	std::vector<StdString> scalarList = grid->getScalarList();
1501
1502	StdString timeid = getTimeCounterName();
1503	StdString dimXid,dimYid;
1504	std::deque<StdString> dimIdList, dimCoordList;
1505	bool hasArea = false;
1506	StdString cellMeasures = "area:";
1507	bool compressedOutput = !field->indexed_output.isEmpty() && field->indexed_output;
1508
1509	for (int i = 0; i < numElement; ++i)
1510	{
1511	if (2 == axisDomainOrder(i))
1512	{
1513	CDomain* domain = CDomain::get(domainList[idxDomain]);
1514	StdString domId = domain->getDomainOutputName();
1515	StdString appendDomId = singleDomain ? "" : "_" + domId ;
1516
1517	if (compressedOutput && domain->isCompressible() && domain->type != CDomain::type_attr::unstructured)
1518	{
1519	dimIdList.push_back(domId + "_points");
1520	field->setUseCompressedOutput();
1521	}
1522
1523	switch (domain->type)
1524	{
1525	case CDomain::type_attr::curvilinear:
1526	if (!compressedOutput \|\| !domain->isCompressible())
1527	{
1528	dimXid = StdString("x").append(appendDomId);
1529	dimIdList.push_back(dimXid);
1530	dimYid = StdString("y").append(appendDomId);
1531	dimIdList.push_back(dimYid);
1532	}
1533	dimCoordList.push_back(StdString("nav_lon").append(appendDomId));
1534	dimCoordList.push_back(StdString("nav_lat").append(appendDomId));
1535	break ;
1536	case CDomain::type_attr::rectilinear:
1537	if (!compressedOutput \|\| !domain->isCompressible())
1538	{
1539	dimXid = StdString("lon").append(appendDomId);
1540	dimIdList.push_back(dimXid);
1541	dimYid = StdString("lat").append(appendDomId);
1542	dimIdList.push_back(dimYid);
1543	}
1544	break ;
1545	case CDomain::type_attr::unstructured:
1546	{
1547	if (SuperClassWriter::useCFConvention)
1548	{
1549	dimXid = StdString("cell").append(appendDomId);
1550	dimIdList.push_back(dimXid);
1551	dimCoordList.push_back(StdString("lon").append(appendDomId));
1552	dimCoordList.push_back(StdString("lat").append(appendDomId));
1553	}
1554	else
1555	{
1556	StdString domainName = domain->name;
1557	if (domain->nvertex == 1)
1558	{
1559	dimXid = "n" + domainName + "_node";
1560	dimIdList.push_back(dimXid);
1561	dimCoordList.push_back(StdString(domainName + "_node_x"));
1562	dimCoordList.push_back(StdString(domainName + "_node_y"));
1563	}
1564	else if (domain->nvertex == 2)
1565	{
1566	dimXid = "n" + domainName + "_edge";
1567	dimIdList.push_back(dimXid);
1568	dimCoordList.push_back(StdString(domainName + "_edge_x"));
1569	dimCoordList.push_back(StdString(domainName + "_edge_y"));
1570	}
1571	else
1572	{
1573	dimXid = "n" + domainName + "_face";
1574	dimIdList.push_back(dimXid);
1575	dimCoordList.push_back(StdString(domainName + "_face_x"));
1576	dimCoordList.push_back(StdString(domainName + "_face_y"));
1577	}
1578	} // ugrid convention
1579	} // case unstructured domain
1580	}
1581
1582	if (domain->hasArea)
1583	{
1584	hasArea = true;
1585	cellMeasures += " area" + appendDomId;
1586	}
1587	++idxDomain;
1588	}
1589	else if (1 == axisDomainOrder(i))
1590	{
1591	CAxis* axis = CAxis::get(axisList[idxAxis]);
1592	StdString axisId = axis->getAxisOutputName();
1593
1594	if (compressedOutput && axis->isCompressible())
1595	{
1596	dimIdList.push_back(axisId + "_points");
1597	field->setUseCompressedOutput();
1598	}
1599	else
1600	dimIdList.push_back(axisId);
1601
1602	dimCoordList.push_back(axisId);
1603	++idxAxis;
1604	}
1605	else // scalar
1606	{
1607	/* Do nothing here */
1608	}
1609	}
1610
1611	/*
1612	StdString lonid_loc = (server->intraCommSize > 1)
1613	? StdString("lon").append(appendDomid).append("_local")
1614	: lonid;
1615	StdString latid_loc = (server->intraCommSize > 1)
1616	? StdString("lat").append(appendDomid).append("_local")
1617	: latid;
1618	*/
1619	StdString fieldid = field->getFieldOutputName();
1620
1621	nc_type type ;
1622	if (field->prec.isEmpty()) type = NC_FLOAT ;
1623	else
1624	{
1625	if (field->prec==2) type = NC_SHORT ;
1626	else if (field->prec==4) type = NC_FLOAT ;
1627	else if (field->prec==8) type = NC_DOUBLE ;
1628	}
1629
1630	bool wtime = !(!field->operation.isEmpty() && field->getOperationTimeType() == func::CFunctor::once);
1631
1632	if (wtime)
1633	{
1634
1635	//StdOStringStream oss;
1636	// oss << "time_" << field->operation.getValue()
1637	// << "_" << field->getRelFile()->output_freq.getValue();
1638	//oss
1639	if (field->getOperationTimeType() == func::CFunctor::instant) coodinates.push_back(string("time_instant"));
1640	else if (field->getOperationTimeType() == func::CFunctor::centered) coodinates.push_back(string("time_centered"));
1641	dims.push_back(timeid);
1642	}
1643
1644	if (compressedOutput && grid->isCompressible())
1645	{
1646	dims.push_back(grid->getId() + "_points");
1647	field->setUseCompressedOutput();
1648	}
1649	else
1650	{
1651	while (!dimIdList.empty())
1652	{
1653	dims.push_back(dimIdList.back());
1654	dimIdList.pop_back();
1655	}
1656	}
1657
1658	while (!dimCoordList.empty())
1659	{
1660	coodinates.push_back(dimCoordList.back());
1661	dimCoordList.pop_back();
1662	}
1663
1664	try
1665	{
1666	SuperClassWriter::addVariable(fieldid, type, dims);
1667
1668	if (!field->standard_name.isEmpty())
1669	SuperClassWriter::addAttribute
1670	("standard_name", field->standard_name.getValue(), &fieldid);
1671
1672	if (!field->long_name.isEmpty())
1673	SuperClassWriter::addAttribute
1674	("long_name", field->long_name.getValue(), &fieldid);
1675
1676	if (!field->unit.isEmpty())
1677	SuperClassWriter::addAttribute
1678	("units", field->unit.getValue(), &fieldid);
1679
1680	// Ugrid field attributes "mesh" and "location"
1681	if (!SuperClassWriter::useCFConvention)
1682	{
1683	if (!domainList.empty())
1684	{
1685	CDomain* domain = CDomain::get(domainList[0]); // Suppose that we have only domain
1686	StdString mesh = domain->name;
1687	SuperClassWriter::addAttribute("mesh", mesh, &fieldid);
1688	StdString location;
1689	if (domain->nvertex == 1)
1690	location = "node";
1691	else if (domain->nvertex == 2)
1692	location = "edge";
1693	else if (domain->nvertex > 2)
1694	location = "face";
1695	SuperClassWriter::addAttribute("location", location, &fieldid);
1696	}
1697
1698	}
1699
1700	if (!field->valid_min.isEmpty())
1701	SuperClassWriter::addAttribute
1702	("valid_min", field->valid_min.getValue(), &fieldid);
1703
1704	if (!field->valid_max.isEmpty())
1705	SuperClassWriter::addAttribute
1706	("valid_max", field->valid_max.getValue(), &fieldid);
1707
1708	if (!field->scale_factor.isEmpty())
1709	SuperClassWriter::addAttribute
1710	("scale_factor", field->scale_factor.getValue(), &fieldid);
1711
1712	if (!field->add_offset.isEmpty())
1713	SuperClassWriter::addAttribute
1714	("add_offset", field->add_offset.getValue(), &fieldid);
1715
1716	SuperClassWriter::addAttribute
1717	("online_operation", field->operation.getValue(), &fieldid);
1718
1719	// write child variables as attributes
1720
1721
1722	vector<CVariable*> listVars = field->getAllVariables() ;
1723	for (vector<CVariable>::iterator it = listVars.begin() ;it != listVars.end(); it++) writeAttribute_(it, fieldid) ;
1724
1725	bool alreadyAddCellMethod = false;
1726	StdString cellMethodsPrefix(""), cellMethodsSuffix("");
1727	if (!field->cell_methods.isEmpty())
1728	{
1729	StdString cellMethodString = field->cell_methods;
1730	if (field->cell_methods_mode.isEmpty() \|\|
1731	(CField::cell_methods_mode_attr::overwrite == field->cell_methods_mode))
1732	{
1733	SuperClassWriter::addAttribute("cell_methods", cellMethodString, &fieldid);
1734	alreadyAddCellMethod = true;
1735	}
1736	else
1737	{
1738	switch (field->cell_methods_mode)
1739	{
1740	case (CField::cell_methods_mode_attr::prefix):
1741	cellMethodsPrefix = cellMethodString;
1742	cellMethodsPrefix += " ";
1743	break;
1744	case (CField::cell_methods_mode_attr::suffix):
1745	cellMethodsSuffix = " ";
1746	cellMethodsSuffix += cellMethodString;
1747	break;
1748	case (CField::cell_methods_mode_attr::none):
1749	break;
1750	default:
1751	break;
1752	}
1753	}
1754	}
1755
1756
1757	if (wtime)
1758	{
1759	CDuration freqOp = field->freq_op.getValue();
1760	freqOp.solveTimeStep(*context->calendar);
1761	StdString freqOpStr = freqOp.toStringUDUnits();
1762	SuperClassWriter::addAttribute("interval_operation", freqOpStr, &fieldid);
1763
1764	CDuration freqOut = field->getRelFile()->output_freq.getValue();
1765	freqOut.solveTimeStep(*context->calendar);
1766	SuperClassWriter::addAttribute("interval_write", freqOut.toStringUDUnits(), &fieldid);
1767
1768	StdString cellMethods(cellMethodsPrefix + "time: ");
1769	if (field->operation.getValue() == "instant") cellMethods += "point";
1770	else if (field->operation.getValue() == "average") cellMethods += "mean";
1771	else if (field->operation.getValue() == "accumulate") cellMethods += "sum";
1772	else cellMethods += field->operation;
1773	if (freqOp.resolve(context->calendar) != freqOut.resolve(context->calendar))
1774	cellMethods += " (interval: " + freqOpStr + ")";
1775	cellMethods += cellMethodsSuffix;
1776	if (!alreadyAddCellMethod)
1777	SuperClassWriter::addAttribute("cell_methods", cellMethods, &fieldid);
1778	}
1779
1780	if (hasArea)
1781	SuperClassWriter::addAttribute("cell_measures", cellMeasures, &fieldid);
1782
1783	if (!field->default_value.isEmpty())
1784	{
1785	double default_value = field->default_value.getValue();
1786	float fdefault_value = (float)default_value;
1787	if (type == NC_DOUBLE)
1788	SuperClassWriter::setDefaultValue(fieldid, &default_value);
1789	else
1790	SuperClassWriter::setDefaultValue(fieldid, &fdefault_value);
1791	}
1792	else
1793	SuperClassWriter::setDefaultValue(fieldid, (double*)NULL);
1794
1795	if (field->compression_level.isEmpty())
1796	field->compression_level = field->file->compression_level.isEmpty() ? 0 : field->file->compression_level;
1797	SuperClassWriter::setCompressionLevel(fieldid, field->compression_level);
1798
1799	{ // Ecriture des coordonnes
1800
1801	StdString coordstr; //boost::algorithm::join(coodinates, " ")
1802	std::vector<StdString>::iterator
1803	itc = coodinates.begin(), endc = coodinates.end();
1804
1805	for (; itc!= endc; itc++)
1806	{
1807	StdString & coord = *itc;
1808	if (itc+1 != endc)
1809	coordstr.append(coord).append(" ");
1810	else coordstr.append(coord);
1811	}
1812
1813	SuperClassWriter::addAttribute("coordinates", coordstr, &fieldid);
1814
1815	}
1816	}
1817	catch (CNetCdfException& e)
1818	{
1819	StdString msg("On writing field : ");
1820	msg.append(fieldid); msg.append("\n");
1821	msg.append("In the context : ");
1822	msg.append(context->getId()); msg.append("\n");
1823	msg.append(e.what());
1824	ERROR("CNc4DataOutput::writeField_(CField* field)", << msg);
1825	}
1826	} // writeField_()
1827
1828	//--------------------------------------------------------------
1829
1830	void CNc4DataOutput::writeFile_ (CFile* file)
1831	{
1832	StdString filename = file->getFileOutputName();
1833	StdString description = (!file->description.isEmpty())
1834	? file->description.getValue()
1835	: StdString("Created by xios");
1836
1837	singleDomain = (file->nbDomains == 1);
1838
1839	try
1840	{
1841	if (SuperClassWriter::useCFConvention)
1842	this->writeFileAttributes(filename, description,
1843	StdString("CF-1.6"),
1844	StdString("An IPSL model"),
1845	this->getTimeStamp());
1846	else
1847	this->writeFileAttributes(filename, description,
1848	StdString("UGRID"),
1849	StdString("An IPSL model"),
1850	this->getTimeStamp());
1851
1852
1853	if (!appendMode)
1854	SuperClassWriter::addDimension("axis_nbounds", 2);
1855	}
1856	catch (CNetCdfException& e)
1857	{
1858	StdString msg("On writing file : ");
1859	msg.append(filename); msg.append("\n");
1860	msg.append("In the context : ");
1861	CContext* context = CContext::getCurrent() ;
1862	msg.append(context->getId()); msg.append("\n");
1863	msg.append(e.what());
1864	ERROR("CNc4DataOutput::writeFile_ (CFile* file)", << msg);
1865	}
1866	}
1867
1868	void CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)
1869	{
1870	StdString name = var->getVariableOutputName();
1871
1872	try
1873	{
1874	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1875	addAttribute(name, var->getData<int>(), &fieldId);
1876	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1877	addAttribute(name, var->getData<short int>(), &fieldId);
1878	else if (var->type.getValue() == CVariable::type_attr::t_float)
1879	addAttribute(name, var->getData<float>(), &fieldId);
1880	else if (var->type.getValue() == CVariable::type_attr::t_double)
1881	addAttribute(name, var->getData<double>(), &fieldId);
1882	else if (var->type.getValue() == CVariable::type_attr::t_string)
1883	addAttribute(name, var->getData<string>(), &fieldId);
1884	else
1885	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)",
1886	<< "Unsupported variable of type " << var->type.getStringValue());
1887	}
1888	catch (CNetCdfException& e)
1889	{
1890	StdString msg("On writing attributes of variable with name : ");
1891	msg.append(name); msg.append("in the field "); msg.append(fieldId); msg.append("\n");
1892	msg.append("In the context : ");
1893	CContext* context = CContext::getCurrent() ;
1894	msg.append(context->getId()); msg.append("\n");
1895	msg.append(e.what());
1896	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var, const string& fieldId)", << msg);
1897	}
1898	}
1899
1900	void CNc4DataOutput::writeAttribute_ (CVariable* var)
1901	{
1902	StdString name = var->getVariableOutputName();
1903
1904	try
1905	{
1906	if (var->type.getValue() == CVariable::type_attr::t_int \|\| var->type.getValue() == CVariable::type_attr::t_int32)
1907	addAttribute(name, var->getData<int>());
1908	else if (var->type.getValue() == CVariable::type_attr::t_int16)
1909	addAttribute(name, var->getData<short int>());
1910	else if (var->type.getValue() == CVariable::type_attr::t_float)
1911	addAttribute(name, var->getData<float>());
1912	else if (var->type.getValue() == CVariable::type_attr::t_double)
1913	addAttribute(name, var->getData<double>());
1914	else if (var->type.getValue() == CVariable::type_attr::t_string)
1915	addAttribute(name, var->getData<string>());
1916	else
1917	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)",
1918	<< "Unsupported variable of type " << var->type.getStringValue());
1919	}
1920	catch (CNetCdfException& e)
1921	{
1922	StdString msg("On writing attributes of variable with name : ");
1923	msg.append(name); msg.append("\n");
1924	msg.append("In the context : ");
1925	CContext* context = CContext::getCurrent() ;
1926	msg.append(context->getId()); msg.append("\n");
1927	msg.append(e.what());
1928	ERROR("CNc4DataOutput::writeAttribute_ (CVariable* var)", << msg);
1929	}
1930	}
1931
1932	void CNc4DataOutput::syncFile_ (void)
1933	{
1934	try
1935	{
1936	SuperClassWriter::sync() ;
1937	}
1938	catch (CNetCdfException& e)
1939	{
1940	StdString msg("On synchronizing the write among processes");
1941	msg.append("In the context : ");
1942	CContext* context = CContext::getCurrent() ;
1943	msg.append(context->getId()); msg.append("\n");
1944	msg.append(e.what());
1945	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1946	}
1947	}
1948
1949	void CNc4DataOutput::closeFile_ (void)
1950	{
1951	try
1952	{
1953	SuperClassWriter::close() ;
1954	}
1955	catch (CNetCdfException& e)
1956	{
1957	StdString msg("On closing file");
1958	msg.append("In the context : ");
1959	CContext* context = CContext::getCurrent() ;
1960	msg.append(context->getId()); msg.append("\n");
1961	msg.append(e.what());
1962	ERROR("CNc4DataOutput::syncFile_ (void)", << msg);
1963	}
1964
1965	}
1966
1967	//---------------------------------------------------------------
1968
1969	StdString CNc4DataOutput::getTimeStamp(void) const
1970	{
1971	const int buffer_size = 100;
1972	time_t rawtime;
1973	struct tm * timeinfo = NULL;
1974	char buffer [buffer_size];
1975	StdString formatStr;
1976	if (file->time_stamp_format.isEmpty()) formatStr="%Y-%b-%d %H:%M:%S %Z" ;
1977	else formatStr=file->time_stamp_format;
1978
1979	// time ( &rawtime );
1980	// timeinfo = localtime ( &rawtime );
1981	time ( &rawtime );
1982	timeinfo = gmtime ( &rawtime );
1983	strftime (buffer, buffer_size, formatStr.c_str(), timeinfo);
1984
1985	return (StdString(buffer));
1986	}
1987
1988	//---------------------------------------------------------------
1989
1990	void CNc4DataOutput::writeFieldData_ (CField* field)
1991	{
1992	CContext* context = CContext::getCurrent();
1993	CContextServer* server = context->server;
1994	CGrid* grid = field->grid;
1995
1996	if (field->getNStep()<1) return ;
1997
1998	if (!grid->doGridHaveDataToWrite())
1999	if (SuperClass::type == MULTI_FILE \|\| !isCollective) return;
2000
2001	StdString fieldid = field->getFieldOutputName();
2002
2003	StdOStringStream oss;
2004	string timeAxisId;
2005	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisId = "time_instant";
2006	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisId = "time_centered";
2007
2008	StdString timeBoundId = getTimeCounterName() + "_bounds";
2009
2010	StdString timeAxisBoundId;
2011	if (field->getOperationTimeType() == func::CFunctor::instant) timeAxisBoundId = "time_instant_bounds";
2012	else if (field->getOperationTimeType() == func::CFunctor::centered) timeAxisBoundId = "time_centered_bounds";
2013
2014	if (!field->wasWritten())
2015	{
2016	if (appendMode && field->file->record_offset.isEmpty() &&
2017	field->getOperationTimeType() != func::CFunctor::once)
2018	{
2019	double factorUnit;
2020	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2021	factorUnit=context->getCalendar()->getDayLengthInSeconds() ;
2022	else factorUnit=1 ;
2023	field->resetNStep(getRecordFromTime(field->last_Write_srv,factorUnit) + 1);
2024	}
2025
2026	field->setWritten();
2027	}
2028
2029
2030	CArray<double,1> time_data(1);
2031	CArray<double,1> time_data_bound(2);
2032	CArray<double,1> time_counter(1);
2033	CArray<double,1> time_counter_bound(2);
2034
2035	bool wtime = (field->getOperationTimeType() != func::CFunctor::once);
2036
2037	if (wtime)
2038	{
2039	Time lastWrite = field->last_Write_srv;
2040	Time lastLastWrite = field->lastlast_Write_srv;
2041
2042	if (field->getOperationTimeType() == func::CFunctor::instant)
2043	time_data(0) = lastWrite;
2044	else if (field->getOperationTimeType() == func::CFunctor::centered)
2045	time_data(0) = (lastWrite + lastLastWrite) / 2;
2046
2047	if (field->getOperationTimeType() == func::CFunctor::instant)
2048	time_data_bound(0) = time_data_bound(1) = lastWrite;
2049	else if (field->getOperationTimeType() == func::CFunctor::centered)
2050	{
2051	time_data_bound(0) = lastLastWrite;
2052	time_data_bound(1) = lastWrite;
2053	}
2054
2055	if (field->file->time_counter.isEmpty())
2056	if (field->hasTimeInstant && !field->hasTimeCentered)
2057	time_counter(0) = lastWrite;
2058	else
2059	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2060
2061	else if (field->file->time_counter == CFile::time_counter_attr::instant)
2062	time_counter(0) = lastWrite;
2063	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2064	time_counter(0) = (lastWrite + lastLastWrite) / 2;
2065	else if (field->file->time_counter == CFile::time_counter_attr::record)
2066	time_counter(0) = field->getNStep() - 1;
2067
2068
2069	if (field->file->time_counter.isEmpty())
2070	if (field->hasTimeInstant && !field->hasTimeCentered)
2071	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2072	else
2073	{
2074	time_counter_bound(0) = lastLastWrite;
2075	time_counter_bound(1) = lastWrite;
2076	}
2077	else if (field->file->time_counter == CFile::time_counter_attr::instant)
2078	time_counter_bound(0) = time_counter_bound(1) = lastWrite;
2079	else if (field->file->time_counter == CFile::time_counter_attr::centered)
2080	{
2081	time_counter_bound(0) = lastLastWrite;
2082	time_counter_bound(1) = lastWrite;
2083	}
2084	else if (field->file->time_counter == CFile::time_counter_attr::record)
2085	time_counter_bound(0) = time_counter_bound(1) = field->getNStep() - 1;
2086
2087
2088
2089	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days)
2090	{
2091	double secByDay=context->getCalendar()->getDayLengthInSeconds() ;
2092	time_data/=secByDay;
2093	time_data_bound/=secByDay;
2094	time_counter/=secByDay;
2095	time_counter_bound/=secByDay;
2096	}
2097	}
2098
2099	bool isRoot = (server->intraCommRank == 0);
2100
2101	if (!field->scale_factor.isEmpty() \|\| !field->add_offset.isEmpty())
2102	{
2103	double scaleFactor = 1.0;
2104	double addOffset = 0.0;
2105	if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor;
2106	if (!field->add_offset.isEmpty()) addOffset = field->add_offset;
2107	field->scaleFactorAddOffset(scaleFactor, addOffset);
2108	}
2109
2110	try
2111	{
2112	size_t writtenSize;
2113	if (field->getUseCompressedOutput())
2114	writtenSize = grid->getNumberWrittenIndexes();
2115	else
2116	writtenSize = grid->getWrittenDataSize();
2117
2118	CArray<double,1> fieldData(writtenSize);
2119	if (!field->default_value.isEmpty()) fieldData = field->default_value;
2120
2121	if (field->getUseCompressedOutput())
2122	field->outputCompressedField(fieldData);
2123	else
2124	field->outputField(fieldData);
2125
2126	if (!field->prec.isEmpty() && field->prec == 2) fieldData = round(fieldData);
2127
2128	switch (SuperClass::type)
2129	{
2130	case (MULTI_FILE) :
2131	{
2132	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1);
2133	if (wtime)
2134	{
2135	SuperClassWriter::writeData(time_data, timeAxisId, isCollective, field->getNStep() - 1);
2136	SuperClassWriter::writeData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1);
2137	if (field->file->time_counter.isEmpty() \|\|
2138	(field->file->time_counter != CFile::time_counter_attr::none))
2139	{
2140	SuperClassWriter::writeData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1);
2141	if (field->file->time_counter.isEmpty() \|\|
2142	(field->file->time_counter != CFile::time_counter_attr::record))
2143	SuperClassWriter::writeData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1);
2144	}
2145	}
2146	break;
2147	}
2148	case (ONE_FILE) :
2149	{
2150	const std::vector<int>& nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal();
2151	const std::vector<int>& nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer();
2152	const std::vector<int>& nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer();
2153
2154	std::vector<StdSize> start, count;
2155
2156	if (field->getUseCompressedOutput())
2157	{
2158	if (grid->isCompressible())
2159	{
2160	start.push_back(grid->getOffsetWrittenIndexes());
2161	count.push_back(grid->getNumberWrittenIndexes());
2162	}
2163	else
2164	{
2165	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2166	std::vector<StdString> domainList = grid->getDomainList();
2167	std::vector<StdString> axisList = grid->getAxisList();
2168	int numElement = axisDomainOrder.numElements();
2169	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2170	int idx = nZoomBeginGlobal.size() - 1;
2171
2172	start.reserve(nZoomBeginGlobal.size());
2173	count.reserve(nZoomBeginGlobal.size());
2174
2175
2176	for (int i = numElement - 1; i >= 0; --i)
2177	{
2178	if (2 == axisDomainOrder(i))
2179	{
2180	CDomain* domain = CDomain::get(domainList[idxDomain]);
2181
2182	if (domain->isCompressible())
2183	{
2184	start.push_back(domain->getOffsetWrittenIndexes());
2185	count.push_back(domain->getNumberWrittenIndexes());
2186	idx -= 2;
2187	}
2188	else
2189	{
2190	if ((domain->type) != CDomain::type_attr::unstructured)
2191	{
2192	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2193	count.push_back(nZoomSizeServer[idx]);
2194	}
2195	--idx;
2196	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2197	count.push_back(nZoomSizeServer[idx]);
2198	--idx;
2199	}
2200	--idxDomain;
2201	}
2202	else if (1 == axisDomainOrder(i))
2203	{
2204	CAxis* axis = CAxis::get(axisList[idxAxis]);
2205
2206	if (axis->isCompressible())
2207	{
2208	start.push_back(axis->getOffsetWrittenIndexes());
2209	count.push_back(axis->getNumberWrittenIndexes());
2210	}
2211	else
2212	{
2213	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2214	count.push_back(nZoomSizeServer[idx]);
2215	}
2216
2217	--idxAxis;
2218	--idx;
2219	}
2220	}
2221	}
2222	}
2223	else
2224	{
2225
2226	CArray<int,1> axisDomainOrder = grid->axis_domain_order;
2227	std::vector<StdString> domainList = grid->getDomainList();
2228	std::vector<StdString> axisList = grid->getAxisList();
2229	int numElement = axisDomainOrder.numElements();
2230	int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1;
2231	int idx = nZoomBeginGlobal.size() - 1;
2232
2233	start.reserve(nZoomBeginGlobal.size());
2234	count.reserve(nZoomBeginGlobal.size());
2235
2236	for (int i = numElement - 1; i >= 0; --i)
2237	{
2238	if (2 == axisDomainOrder(i))
2239	{
2240	CDomain* domain = CDomain::get(domainList[idxDomain]);
2241	if ((domain->type) != CDomain::type_attr::unstructured)
2242	{
2243	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2244	count.push_back(nZoomSizeServer[idx]);
2245	}
2246	--idx ;
2247	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2248	count.push_back(nZoomSizeServer[idx]);
2249	--idx ;
2250	--idxDomain;
2251	}
2252	else if (1 == axisDomainOrder(i))
2253	{
2254	start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]);
2255	count.push_back(nZoomSizeServer[idx]);
2256	--idx;
2257	}
2258	else
2259	{
2260	if (1 == axisDomainOrder.numElements())
2261	{
2262	start.push_back(0);
2263	count.push_back(1);
2264	}
2265	--idx;
2266	}
2267	}
2268	}
2269
2270	SuperClassWriter::writeData(fieldData, fieldid, isCollective, field->getNStep() - 1, &start, &count);
2271	if (wtime)
2272	{
2273	SuperClassWriter::writeTimeAxisData(time_data, timeAxisId, isCollective, field->getNStep() - 1, isRoot);
2274	SuperClassWriter::writeTimeAxisData(time_data_bound, timeAxisBoundId, isCollective, field->getNStep() - 1, isRoot);
2275	if (field->file->time_counter.isEmpty() \|\|
2276	(field->file->time_counter != CFile::time_counter_attr::none))
2277	{
2278	SuperClassWriter::writeTimeAxisData(time_counter, getTimeCounterName(), isCollective, field->getNStep() - 1, isRoot);
2279	if (field->file->time_counter.isEmpty() \|\|
2280	(field->file->time_counter != CFile::time_counter_attr::record))
2281	SuperClassWriter::writeTimeAxisData(time_counter_bound, timeBoundId, isCollective, field->getNStep() - 1, isRoot);
2282	}
2283	}
2284
2285	break;
2286	}
2287	}
2288	}
2289	catch (CNetCdfException& e)
2290	{
2291	StdString msg("On writing field data: ");
2292	msg.append(fieldid); msg.append("\n");
2293	msg.append("In the context : ");
2294	msg.append(context->getId()); msg.append("\n");
2295	msg.append(e.what());
2296	ERROR("CNc4DataOutput::writeFieldData_ (CField* field)", << msg);
2297	}
2298	}
2299
2300	//---------------------------------------------------------------
2301
2302	void CNc4DataOutput::writeTimeAxis_
2303	(CField* field,
2304	const boost::shared_ptr<CCalendar> cal)
2305	{
2306	StdOStringStream oss;
2307
2308	if (field->getOperationTimeType() == func::CFunctor::once) return ;
2309
2310	// oss << "time_" << field->operation.getValue()
2311	// << "_" << field->getRelFile()->output_freq.getValue();
2312
2313	// StdString axisid = oss.str();
2314	// if (field->getOperationTimeType() == func::CFunctor::centered) axisid="time_centered" ;
2315	// else if (field->getOperationTimeType() == func::CFunctor::instant) axisid="time_instant" ;
2316
2317	StdString axisid("time_centered") ;
2318	StdString axisBoundId("time_centered_bounds");
2319	StdString timeid(getTimeCounterName());
2320	StdString timeBoundId("axis_nbounds");
2321
2322	StdString strTimeUnits ;
2323	if (!field->file->time_units.isEmpty() && field->file->time_units==CFile::time_units_attr::days) strTimeUnits="days since " ;
2324	else strTimeUnits="seconds since " ;
2325
2326	if (field->getOperationTimeType() == func::CFunctor::instant)
2327	{
2328	axisid = "time_instant";
2329	axisBoundId = "time_instant_bounds";
2330	field->hasTimeInstant = true;
2331	}
2332
2333	if (field->getOperationTimeType() == func::CFunctor::centered)
2334	{
2335	field->hasTimeCentered = true;
2336	}
2337
2338	try
2339	{
2340	// Adding time_instant or time_centered
2341	std::vector<StdString> dims;
2342	dims.push_back(timeid);
2343	if (!SuperClassWriter::varExist(axisid))
2344	{
2345	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2346
2347	CDate timeOrigin=cal->getTimeOrigin() ;
2348	StdOStringStream oss2;
2349	// oss2<<initDate.getYear()<<"-"<<initDate.getMonth()<<"-"<<initDate.getDay()<<" "
2350	// <<initDate.getHour()<<"-"<<initDate.getMinute()<<"-"<<initDate.getSecond() ;
2351	StdString strInitdate=oss2.str() ;
2352	StdString strTimeOrigin=timeOrigin.toString() ;
2353	this->writeTimeAxisAttributes
2354	(axisid, cal->getType(),strTimeUnits+strTimeOrigin,
2355	strTimeOrigin, axisBoundId);
2356	}
2357
2358	// Adding time_instant_bounds or time_centered_bounds variables
2359	if (!SuperClassWriter::varExist(axisBoundId))
2360	{
2361	dims.clear() ;
2362	dims.push_back(timeid);
2363	dims.push_back(timeBoundId);
2364	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2365	}
2366
2367	if (field->file->time_counter.isEmpty() \|\|
2368	(field->file->time_counter != CFile::time_counter_attr::none))
2369	{
2370	// Adding time_counter
2371	axisid = getTimeCounterName();
2372	axisBoundId = getTimeCounterName() + "_bounds";
2373	dims.clear();
2374	dims.push_back(timeid);
2375	if (!SuperClassWriter::varExist(axisid))
2376	{
2377	SuperClassWriter::addVariable(axisid, NC_DOUBLE, dims);
2378	SuperClassWriter::addAttribute("axis", string("T"), &axisid);
2379
2380	if (field->file->time_counter.isEmpty() \|\|
2381	(field->file->time_counter != CFile::time_counter_attr::record))
2382	{
2383	CDate timeOrigin = cal->getTimeOrigin();
2384	StdString strTimeOrigin = timeOrigin.toString();
2385
2386	this->writeTimeAxisAttributes(axisid, cal->getType(),
2387	strTimeUnits+strTimeOrigin,
2388	strTimeOrigin, axisBoundId);
2389	}
2390	}
2391
2392	// Adding time_counter_bound dimension
2393	if (field->file->time_counter.isEmpty() \|\|
2394	(field->file->time_counter != CFile::time_counter_attr::record))
2395	{
2396	if (!SuperClassWriter::varExist(axisBoundId))
2397	{
2398	dims.clear();
2399	dims.push_back(timeid);
2400	dims.push_back(timeBoundId);
2401	SuperClassWriter::addVariable(axisBoundId, NC_DOUBLE, dims);
2402	}
2403	}
2404	}
2405	}
2406	catch (CNetCdfException& e)
2407	{
2408	StdString msg("On writing time axis data: ");
2409	msg.append("In the context : ");
2410	CContext* context = CContext::getCurrent() ;
2411	msg.append(context->getId()); msg.append("\n");
2412	msg.append(e.what());
2413	ERROR("CNc4DataOutput::writeTimeAxis_ (CField* field, \
2414	const boost::shared_ptr<CCalendar> cal)", << msg);
2415	}
2416	}
2417
2418	//---------------------------------------------------------------
2419
2420	void CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name,
2421	const StdString & calendar,
2422	const StdString & units,
2423	const StdString & time_origin,
2424	const StdString & time_bounds,
2425	const StdString & standard_name,
2426	const StdString & long_name)
2427	{
2428	try
2429	{
2430	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2431	SuperClassWriter::addAttribute("long_name", long_name , &axis_name);
2432	SuperClassWriter::addAttribute("calendar", calendar , &axis_name);
2433	SuperClassWriter::addAttribute("units", units , &axis_name);
2434	SuperClassWriter::addAttribute("time_origin", time_origin , &axis_name);
2435	SuperClassWriter::addAttribute("bounds", time_bounds , &axis_name);
2436	}
2437	catch (CNetCdfException& e)
2438	{
2439	StdString msg("On writing time axis Attribute: ");
2440	msg.append("In the context : ");
2441	CContext* context = CContext::getCurrent() ;
2442	msg.append(context->getId()); msg.append("\n");
2443	msg.append(e.what());
2444	ERROR("CNc4DataOutput::writeTimeAxisAttributes(const StdString & axis_name, \
2445	const StdString & calendar,\
2446	const StdString & units, \
2447	const StdString & time_origin, \
2448	const StdString & time_bounds, \
2449	const StdString & standard_name, \
2450	const StdString & long_name)", << msg);
2451	}
2452	}
2453
2454	//---------------------------------------------------------------
2455
2456	void CNc4DataOutput::writeAxisAttributes(const StdString & axis_name,
2457	const StdString & axis,
2458	const StdString & standard_name,
2459	const StdString & long_name,
2460	const StdString & units,
2461	const StdString & nav_model)
2462	{
2463	try
2464	{
2465	if (!axis.empty())
2466	SuperClassWriter::addAttribute("axis" , axis , &axis_name);
2467
2468	SuperClassWriter::addAttribute("standard_name", standard_name, &axis_name);
2469	SuperClassWriter::addAttribute("long_name" , long_name , &axis_name);
2470	SuperClassWriter::addAttribute("units" , units , &axis_name);
2471	// SuperClassWriter::addAttribute("nav_model" , nav_model , &axis_name);
2472	}
2473	catch (CNetCdfException& e)
2474	{
2475	StdString msg("On writing Axis Attribute: ");
2476	msg.append("In the context : ");
2477	CContext* context = CContext::getCurrent() ;
2478	msg.append(context->getId()); msg.append("\n");
2479	msg.append(e.what());
2480	ERROR("CNc4DataOutput::writeAxisAttributes(const StdString & axis_name, \
2481	const StdString & axis, \
2482	const StdString & standard_name, \
2483	const StdString & long_name, \
2484	const StdString & units, \
2485	const StdString & nav_model)", << msg);
2486	}
2487	}
2488
2489	//---------------------------------------------------------------
2490
2491	void CNc4DataOutput::writeLocalAttributes
2492	(int ibegin, int ni, int jbegin, int nj, StdString domid)
2493	{
2494	try
2495	{
2496	SuperClassWriter::addAttribute(StdString("ibegin").append(domid), ibegin);
2497	SuperClassWriter::addAttribute(StdString("ni" ).append(domid), ni);
2498	SuperClassWriter::addAttribute(StdString("jbegin").append(domid), jbegin);
2499	SuperClassWriter::addAttribute(StdString("nj" ).append(domid), nj);
2500	}
2501	catch (CNetCdfException& e)
2502	{
2503	StdString msg("On writing Local Attributes: ");
2504	msg.append("In the context : ");
2505	CContext* context = CContext::getCurrent() ;
2506	msg.append(context->getId()); msg.append("\n");
2507	msg.append(e.what());
2508	ERROR("CNc4DataOutput::writeLocalAttributes \
2509	(int ibegin, int ni, int jbegin, int nj, StdString domid)", << msg);
2510	}
2511
2512	}
2513
2514	void CNc4DataOutput::writeLocalAttributes_IOIPSL(const StdString& dimXid, const StdString& dimYid,
2515	int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)
2516	{
2517	CArray<int,1> array(2) ;
2518
2519	try
2520	{
2521	SuperClassWriter::addAttribute("DOMAIN_number_total",size ) ;
2522	SuperClassWriter::addAttribute("DOMAIN_number", rank) ;
2523	array = SuperClassWriter::getDimension(dimXid) + 1, SuperClassWriter::getDimension(dimYid) + 1;
2524	SuperClassWriter::addAttribute("DOMAIN_dimensions_ids",array) ;
2525	array=ni_glo,nj_glo ;
2526	SuperClassWriter::addAttribute("DOMAIN_size_global", array) ;
2527	array=ni,nj ;
2528	SuperClassWriter::addAttribute("DOMAIN_size_local", array) ;
2529	array=ibegin+1,jbegin+1 ;
2530	SuperClassWriter::addAttribute("DOMAIN_position_first", array) ;
2531	array=ibegin+ni-1+1,jbegin+nj-1+1 ;
2532	SuperClassWriter::addAttribute("DOMAIN_position_last",array) ;
2533	array=0,0 ;
2534	SuperClassWriter::addAttribute("DOMAIN_halo_size_start", array) ;
2535	SuperClassWriter::addAttribute("DOMAIN_halo_size_end", array);
2536	SuperClassWriter::addAttribute("DOMAIN_type",string("box")) ;
2537	/*
2538	SuperClassWriter::addAttribute("DOMAIN_DIM_N001",string("x")) ;
2539	SuperClassWriter::addAttribute("DOMAIN_DIM_N002",string("y")) ;
2540	SuperClassWriter::addAttribute("DOMAIN_DIM_N003",string("axis_A")) ;
2541	SuperClassWriter::addAttribute("DOMAIN_DIM_N004",string("time_counter")) ;
2542	*/
2543	}
2544	catch (CNetCdfException& e)
2545	{
2546	StdString msg("On writing Local Attributes IOIPSL \n");
2547	msg.append("In the context : ");
2548	CContext* context = CContext::getCurrent() ;
2549	msg.append(context->getId()); msg.append("\n");
2550	msg.append(e.what());
2551	ERROR("CNc4DataOutput::writeLocalAttributes_IOIPSL \
2552	(int ibegin, int ni, int jbegin, int nj, int ni_glo, int nj_glo, int rank, int size)", << msg);
2553	}
2554	}
2555	//---------------------------------------------------------------
2556
2557	void CNc4DataOutput:: writeFileAttributes(const StdString & name,
2558	const StdString & description,
2559	const StdString & conventions,
2560	const StdString & production,
2561	const StdString & timeStamp)
2562	{
2563	try
2564	{
2565	SuperClassWriter::addAttribute("name" , name);
2566	SuperClassWriter::addAttribute("description", description);
2567	SuperClassWriter::addAttribute("title" , description);
2568	SuperClassWriter::addAttribute("Conventions", conventions);
2569	// SuperClassWriter::addAttribute("production" , production);
2570	StdString timeStampStr ;
2571	if (file->time_stamp_name.isEmpty()) timeStampStr="timeStamp" ;
2572	else timeStampStr=file->time_stamp_name ;
2573	SuperClassWriter::addAttribute(timeStampStr, timeStamp);
2574	}
2575	catch (CNetCdfException& e)
2576	{
2577	StdString msg("On writing File Attributes \n ");
2578	msg.append("In the context : ");
2579	CContext* context = CContext::getCurrent() ;
2580	msg.append(context->getId()); msg.append("\n");
2581	msg.append(e.what());
2582	ERROR("CNc4DataOutput:: writeFileAttributes(const StdString & name, \
2583	const StdString & description, \
2584	const StdString & conventions, \
2585	const StdString & production, \
2586	const StdString & timeStamp)", << msg);
2587	}
2588	}
2589
2590	//---------------------------------------------------------------
2591
2592	void CNc4DataOutput::writeMaskAttributes(const StdString & mask_name,
2593	int data_dim,
2594	int data_ni,
2595	int data_nj,
2596	int data_ibegin,
2597	int data_jbegin)
2598	{
2599	try
2600	{
2601	SuperClassWriter::addAttribute("data_dim" , data_dim , &mask_name);
2602	SuperClassWriter::addAttribute("data_ni" , data_ni , &mask_name);
2603	SuperClassWriter::addAttribute("data_nj" , data_nj , &mask_name);
2604	SuperClassWriter::addAttribute("data_ibegin", data_ibegin, &mask_name);
2605	SuperClassWriter::addAttribute("data_jbegin", data_jbegin, &mask_name);
2606	}
2607	catch (CNetCdfException& e)
2608	{
2609	StdString msg("On writing Mask Attributes \n ");
2610	msg.append("In the context : ");
2611	CContext* context = CContext::getCurrent() ;
2612	msg.append(context->getId()); msg.append("\n");
2613	msg.append(e.what());
2614	ERROR("CNc4DataOutput::writeMaskAttributes(const StdString & mask_name, \
2615	int data_dim, \
2616	int data_ni, \
2617	int data_nj, \
2618	int data_ibegin, \
2619	int data_jbegin)", << msg);
2620	}
2621	}
2622
2623	///--------------------------------------------------------------
2624
2625	StdSize CNc4DataOutput::getRecordFromTime(Time time, double factorUnit)
2626	{
2627	std::map<Time, StdSize>::const_iterator it = timeToRecordCache.find(time);
2628	if (it == timeToRecordCache.end())
2629	{
2630	StdString timeAxisBoundsId(getTimeCounterName() + "_bounds");
2631	if (!SuperClassWriter::varExist(timeAxisBoundsId))
2632	timeAxisBoundsId = "time_instant_bounds";
2633
2634	CArray<double,2> timeAxisBounds;
2635	SuperClassWriter::getTimeAxisBounds(timeAxisBounds, timeAxisBoundsId, isCollective);
2636	timeAxisBounds*=factorUnit ;
2637
2638	StdSize record = 0;
2639	double dtime(time);
2640	for (int n = timeAxisBounds.extent(1) - 1; n >= 0; n--)
2641	{
2642	if (timeAxisBounds(1, n) < dtime)
2643	{
2644	record = n + 1;
2645	break;
2646	}
2647	}
2648	it = timeToRecordCache.insert(std::make_pair(time, record)).first;
2649	}
2650	return it->second;
2651	}
2652
2653	///--------------------------------------------------------------
2654
2655	bool CNc4DataOutput::isWrittenDomain(const std::string& domainName) const
2656	{
2657	return (this->writtenDomains.find(domainName) != this->writtenDomains.end());
2658	}
2659
2660	bool CNc4DataOutput::isWrittenCompressedDomain(const std::string& domainName) const
2661	{
2662	return (this->writtenCompressedDomains.find(domainName) != this->writtenCompressedDomains.end());
2663	}
2664
2665	bool CNc4DataOutput::isWrittenAxis(const std::string& axisName) const
2666	{
2667	return (this->writtenAxis.find(axisName) != this->writtenAxis.end());
2668	}
2669
2670	bool CNc4DataOutput::isWrittenCompressedAxis(const std::string& axisName) const
2671	{
2672	return (this->writtenCompressedAxis.find(axisName) != this->writtenCompressedAxis.end());
2673	}
2674
2675	bool CNc4DataOutput::isWrittenScalar(const std::string& scalarName) const
2676	{
2677	return (this->writtenScalar.find(scalarName) != this->writtenScalar.end());
2678	}
2679
2680	void CNc4DataOutput::setWrittenDomain(const std::string& domainName)
2681	{
2682	this->writtenDomains.insert(domainName);
2683	}
2684
2685	void CNc4DataOutput::setWrittenCompressedDomain(const std::string& domainName)
2686	{
2687	this->writtenCompressedDomains.insert(domainName);
2688	}
2689
2690	void CNc4DataOutput::setWrittenAxis(const std::string& axisName)
2691	{
2692	this->writtenAxis.insert(axisName);
2693	}
2694
2695	void CNc4DataOutput::setWrittenCompressedAxis(const std::string& axisName)
2696	{
2697	this->writtenCompressedAxis.insert(axisName);
2698	}
2699
2700	void CNc4DataOutput::setWrittenScalar(const std::string& scalarName)
2701	{
2702	this->writtenScalar.insert(scalarName);
2703	}
2704	} // namespace xios

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source: XIOS/trunk/src/io/nc4_data_output.cpp @ 1046

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